motif conformation finder

find all instances of an amino acid sequence motif in protein structures and parse their internal coordinates

API Documentation

Dependencies

• Python 3.11
• Biopython

Usage:

1. Install dependencies

2. Download the protein structures from the PDB

3. Write chain query file (optional)

   • A list specifying which chains to search, and which protein structure files to search in.
     This file is a long-format csv file containing the protein entry ids, the path to each
     protein file from the root directory that contains all the protein structure files, and
     the chain entry identifiers for each protein file, e.g.
     
     

   Protein ID, File Path, Chain
   1i6w, 1i6w.pdb.ent.gz, A
   1i6w, 1i6w.pdb.ent.gz, B
   1gci, 1gci.pdb.gz, A
   ...        
   

4. Run motif-conformations.py from the command-line:

   ./motif-conformations.py [-h] [-q QUERY_LIST] [-g] motif structure_directory {pdb,cif} output_file
   

   • run ./motif-conformations.py -h or ./motif-conformations.py --help for
     command line usage help.
   • use -q to specify the path to the chain query file you generated above in 3.
     If you do not specify a file, then the program will attempt to parse all files in the
     structure_directory and seek motif in all the protein chains it finds
   • use the -g flag if the protein structure files are gzipped
   • motif is the amino acid sequence to seek. Note that the program currently only
     seeks exact matches, and will not interpret promotif or regex motifs
   • structure_directory is the path of the the root directory that contains all the
     protein structure files
   • choose cif if the protein structure files are in the PDBx/MMCIF (.cif) format
   • choose pdb if the protein structure files are in the .pdb format
   • output_file is the name of the output file that the program will write

🤿 Dive deeper:

Read the API Documentation to take a deeper look at the code.